Merge pull request #231 from AllenNeuralDynamics/release-v0.23.0

Release v0.23.0

src/aind_metadata_mapper/__init__.py

@@ -1,3 +1,3 @@
 """Init package"""
 
-__version__ = "0.22.2"
+__version__ = "0.23.0"

src/aind_metadata_mapper/gather_metadata.py

@@ -18,6 +18,7 @@
 from aind_data_schema.core.metadata import Metadata
 from aind_data_schema.core.procedures import Procedures
 from aind_data_schema.core.processing import PipelineProcess, Processing
+from aind_data_schema.core.quality_control import QualityControl
 from aind_data_schema.core.rig import Rig
 from aind_data_schema.core.session import Session
 from aind_data_schema.core.subject import Subject
@@ -304,6 +305,17 @@ def get_rig_metadata(self) -> Optional[dict]:
         else:
             return None
 
+    def get_quality_control_metadata(self) -> Optional[dict]:
+        """Get quality_control metadata"""
+        file_name = QualityControl.default_filename()
+        if self._does_file_exist_in_user_defined_dir(file_name=file_name):
+            contents = self._get_file_from_user_defined_directory(
+                file_name=file_name
+            )
+            return contents
+        else:
+            return None
+
     def get_acquisition_metadata(self) -> Optional[dict]:
         """Get acquisition metadata"""
         file_name = Acquisition.default_filename()
@@ -388,6 +400,10 @@ def load_model(
             self.settings.metadata_settings.session_filepath, Session
         )
         rig = load_model(self.settings.metadata_settings.rig_filepath, Rig)
+        quality_control = load_model(
+            self.settings.metadata_settings.quality_control_filepath,
+            QualityControl,
+        )
         acquisition = load_model(
             self.settings.metadata_settings.acquisition_filepath, Acquisition
         )
@@ -410,6 +426,7 @@ def load_model(
                 processing=processing,
                 acquisition=acquisition,
                 instrument=instrument,
+                quality_control=quality_control,
             )
             metadata_json = json.loads(metadata.model_dump_json(by_alias=True))
             return metadata_json
@@ -430,6 +447,7 @@ def load_model(
             metadata_json["processing"] = processing
             metadata_json["acquisition"] = acquisition
             metadata_json["instrument"] = instrument
+            metadata_json["quality_control"] = quality_control
             return metadata_json
 
     def _write_json_file(self, filename: str, contents: dict) -> None:

src/aind_metadata_mapper/models.py

@@ -97,6 +97,7 @@ class MetadataSettings(BaseSettings, extra="allow"):
     processing_filepath: Optional[Path] = None
     acquisition_filepath: Optional[Path] = None
     instrument_filepath: Optional[Path] = None
+    quality_control_filepath: Optional[Path] = None
 
 
 class JobSettings(BaseSettings, extra="allow"):

tests/resources/gather_metadata_job/metadata_files/quality_control.json

@@ -0,0 +1,209 @@
+{
+   "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/quality_control.py",
+   "schema_version": "1.2.2",
+   "evaluations": [
+      {
+         "modality": {
+            "name": "Extracellular electrophysiology",
+            "abbreviation": "ecephys"
+         },
+         "stage": "Raw data",
+         "name": "Drift map",
+         "description": "Check that all probes show minimal drift",
+         "metrics": [
+            {
+               "name": "Probe A drift",
+               "value": {
+                  "value": "",
+                  "options": [
+                     "Low",
+                     "Medium",
+                     "High"
+                  ],
+                  "status": [
+                     "Pass",
+                     "Fail",
+                     "Fail"
+                  ],
+                  "type": "dropdown"
+               },
+               "status_history": [
+                  {
+                     "evaluator": "",
+                     "status": "Pending",
+                     "timestamp": "2022-11-22T00:00:00Z"
+                  }
+               ],
+               "description": "Qualitative check that drift map shows minimal movement",
+               "reference": "ecephys-drift-map",
+               "evaluated_assets": null
+            },
+            {
+               "name": "Probe B drift",
+               "value": {
+                  "value": "",
+                  "options": [
+                     "No Drift",
+                     "Drift visible in part of session",
+                     "Drift visible in entire session",
+                     "Sudden movement event"
+                  ],
+                  "status": [
+                     "Pass",
+                     "Pass",
+                     "Fail",
+                     "Fail"
+                  ],
+                  "type": "checkbox"
+               },
+               "status_history": [
+                  {
+                     "evaluator": "",
+                     "status": "Pending",
+                     "timestamp": "2022-11-22T00:00:00Z"
+                  }
+               ],
+               "description": "Qualitative check that drift map shows minimal movement",
+               "reference": "ecephys-drift-map",
+               "evaluated_assets": null
+            },
+            {
+               "name": "Probe C drift",
+               "value": "Low",
+               "status_history": [
+                  {
+                     "evaluator": "Automated",
+                     "status": "Pass",
+                     "timestamp": "2022-11-22T00:00:00Z"
+                  }
+               ],
+               "description": null,
+               "reference": "ecephys-drift-map",
+               "evaluated_assets": null
+            }
+         ],
+         "tags": null,
+         "notes": "",
+         "allow_failed_metrics": false,
+         "latest_status": "Pending",
+         "created": "2022-11-22T00:00:00Z"
+      },
+      {
+         "modality": {
+            "name": "Behavior videos",
+            "abbreviation": "behavior-videos"
+         },
+         "stage": "Raw data",
+         "name": "Video frame count check",
+         "description": null,
+         "metrics": [
+            {
+               "name": "Expected frame count",
+               "value": 662,
+               "status_history": [
+                  {
+                     "evaluator": "Automated",
+                     "status": "Pass",
+                     "timestamp": "2022-11-22T00:00:00Z"
+                  }
+               ],
+               "description": "Expected frame count from experiment length, always pass",
+               "reference": null,
+               "evaluated_assets": null
+            },
+            {
+               "name": "Video 1 frame count",
+               "value": 662,
+               "status_history": [
+                  {
+                     "evaluator": "Automated",
+                     "status": "Pass",
+                     "timestamp": "2022-11-22T00:00:00Z"
+                  }
+               ],
+               "description": "Pass when frame count matches expected",
+               "reference": null,
+               "evaluated_assets": null
+            },
+            {
+               "name": "Video 2 num frames",
+               "value": 662,
+               "status_history": [
+                  {
+                     "evaluator": "Automated",
+                     "status": "Pass",
+                     "timestamp": "2022-11-22T00:00:00Z"
+                  }
+               ],
+               "description": "Pass when frame count matches expected",
+               "reference": null,
+               "evaluated_assets": null
+            }
+         ],
+         "tags": null,
+         "notes": "Pass when video_1_num_frames==video_2_num_frames",
+         "allow_failed_metrics": false,
+         "latest_status": "Pass",
+         "created": "2022-11-22T00:00:00Z"
+      },
+      {
+         "modality": {
+            "name": "Extracellular electrophysiology",
+            "abbreviation": "ecephys"
+         },
+         "stage": "Raw data",
+         "name": "Probes present",
+         "description": "Pass when data from a probe is present",
+         "metrics": [
+            {
+               "name": "ProbeA",
+               "value": true,
+               "status_history": [
+                  {
+                     "evaluator": "Automated",
+                     "status": "Pass",
+                     "timestamp": "2022-11-22T00:00:00Z"
+                  }
+               ],
+               "description": null,
+               "reference": null,
+               "evaluated_assets": null
+            },
+            {
+               "name": "ProbeB",
+               "value": true,
+               "status_history": [
+                  {
+                     "evaluator": "Automated",
+                     "status": "Pass",
+                     "timestamp": "2022-11-22T00:00:00Z"
+                  }
+               ],
+               "description": null,
+               "reference": null,
+               "evaluated_assets": null
+            },
+            {
+               "name": "ProbeC",
+               "value": true,
+               "status_history": [
+                  {
+                     "evaluator": "Automated",
+                     "status": "Pass",
+                     "timestamp": "2022-11-22T00:00:00Z"
+                  }
+               ],
+               "description": null,
+               "reference": null,
+               "evaluated_assets": null
+            }
+         ],
+         "tags": null,
+         "notes": null,
+         "allow_failed_metrics": false,
+         "latest_status": "Pass",
+         "created": "2022-11-22T00:00:00Z"
+      }
+   ],
+   "notes": null
+}

tests/test_gather_metadata.py

@@ -644,6 +644,28 @@ def test_get_rig_metadata_none(self):
         contents = metadata_job.get_rig_metadata()
         self.assertIsNone(contents)
 
+    def test_get_quality_control_metadata(self):
+        """Tests get_quality_control_metadata"""
+        metadata_dir = RESOURCES_DIR / "metadata_files"
+
+        job_settings = JobSettings(
+            directory_to_write_to=RESOURCES_DIR,
+            metadata_dir=metadata_dir,
+        )
+        metadata_job = GatherMetadataJob(settings=job_settings)
+        contents = metadata_job.get_quality_control_metadata()
+        self.assertIsNotNone(contents)
+
+    def test_get_quality_control_metadata_none(self):
+        """Tests get_quality_control_metadata returns none"""
+
+        job_settings = JobSettings(
+            directory_to_write_to=RESOURCES_DIR,
+        )
+        metadata_job = GatherMetadataJob(settings=job_settings)
+        contents = metadata_job.get_quality_control_metadata()
+        self.assertIsNone(contents)
+
     def test_get_problematic_rig_metadata(self):
         """Tests get_rig_metadata when there is a pydantic serialization
         issue."""